Variant report

Variant	rs11870422
Chromosome Location	chr17:16933983-16933984
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16932063..16934977-chr17:16936868..16939174,3	K562	blood:
2	chr17:16931573..16934044-chr17:16934220..16938314,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1047799	0.92[CHD][hapmap]
rs10852842	0.84[EUR][1000 genomes]
rs11078371	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs11078373	0.92[CHD][hapmap]
rs11870483	0.86[EUR][1000 genomes]
rs11870997	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601422	0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2292530	0.92[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap]
rs28452405	0.81[ASN][1000 genomes]
rs34001712	0.81[ASN][1000 genomes]
rs35650871	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3744132	0.92[CHD][hapmap]
rs3744134	0.90[CHD][hapmap]
rs3744137	0.92[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap]
rs3744138	0.92[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap]
rs3744139	0.92[CHD][hapmap]
rs4073688	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs4074612	1.00[JPT][hapmap]
rs4468683	0.84[ASN][1000 genomes]
rs4589617	0.89[ASN][1000 genomes]
rs4629023	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs4641803	0.92[ASN][1000 genomes]
rs4985704	0.92[CHD][hapmap]
rs4985716	0.82[ASN][1000 genomes]
rs4985721	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985730	0.83[EUR][1000 genomes]
rs4985741	0.92[CHD][hapmap]
rs4985742	0.92[CHD][hapmap]
rs57729820	0.83[ASN][1000 genomes]
rs61242604	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7212275	0.82[ASN][1000 genomes]
rs7214429	0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs7218781	0.92[CHD][hapmap]
rs8066234	0.92[CHD][hapmap]
rs8071254	0.83[ASN][1000 genomes]
rs8076273	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9892695	0.93[ASN][1000 genomes]
rs9906028	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9907109	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv543231	chr17:16926227-16950644	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11870422	FLCN	cis	multi-tissue	Pritchard
rs11870422	RAI1	cis	cerebellum	SCAN
rs11870422	TOM1L2	cis	cerebellum	SCAN
rs11870422	FLCN	cis	parietal	SCAN
rs11870422	MPRIP	cis	lymphoblastoid	seeQTL
rs11870422	M-RIP	cis	multi-tissue	Pritchard
rs11870422	FLCN	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16928800-16934000	Enhancers	Fetal Intestine Large	intestine
2	chr17:16930200-16936200	Enhancers	Fetal Muscle Leg	muscle
3	chr17:16930400-16934000	Enhancers	Fetal Intestine Small	intestine
4	chr17:16930400-16934000	Enhancers	Stomach Mucosa	stomach
5	chr17:16930400-16934400	Enhancers	Placenta	Placenta
6	chr17:16930400-16936600	Enhancers	Fetal Muscle Trunk	muscle
7	chr17:16930600-16934400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:16930600-16936000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:16930600-16936200	Enhancers	HMEC	breast
10	chr17:16930600-16937600	Enhancers	HSMMtube	muscle
11	chr17:16930800-16935800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:16930800-16936000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:16931000-16934000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr17:16931000-16934200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr17:16931000-16936000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:16931400-16934400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:16931400-16936000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:16931600-16934200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr17:16931600-16936400	Enhancers	Fetal Lung	lung
20	chr17:16932000-16934000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr17:16932000-16934000	Weak transcription	Psoas Muscle	Psoas
22	chr17:16932000-16934200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:16932000-16934200	Weak transcription	Left Ventricle	heart
24	chr17:16932000-16934200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr17:16932000-16934400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:16932000-16935000	Weak transcription	Brain Angular Gyrus	brain
27	chr17:16932000-16935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:16932200-16935200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr17:16932200-16935200	Weak transcription	NHLF	lung
30	chr17:16932200-16939800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr17:16932400-16934400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr17:16932400-16934400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:16932400-16934400	Weak transcription	Right Atrium	heart
34	chr17:16932400-16934400	Weak transcription	Right Ventricle	heart
35	chr17:16932400-16935200	Weak transcription	Spleen	Spleen
36	chr17:16932400-16940600	Enhancers	HSMM	muscle
37	chr17:16932600-16934600	Weak transcription	NHDF-Ad	bronchial
38	chr17:16932600-16935000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:16932600-16936000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr17:16932800-16934200	Weak transcription	Fetal Stomach	stomach
41	chr17:16932800-16934400	Weak transcription	Pancreas	Pancrea
42	chr17:16932800-16934600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:16932800-16944200	Weak transcription	Fetal Brain Female	brain
44	chr17:16933000-16934000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:16933000-16934200	Weak transcription	Lung	lung
46	chr17:16933000-16935000	Weak transcription	NHEK	skin
47	chr17:16933000-16935200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr17:16933000-16935400	Enhancers	A549	lung
49	chr17:16933000-16935600	Weak transcription	Esophagus	oesophagus
50	chr17:16933200-16934200	Weak transcription	Osteobl	bone

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